diff tools/metag_tools/mapping_to_ucsc.py @ 0:9071e359b9a3

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/metag_tools/mapping_to_ucsc.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,204 @@
+#!/usr/bin/env python
+
+from galaxy import eggs
+import sys, tempfile, os
+
+assert sys.version_info[:2] >= (2.4)
+
+def stop_err(msg):
+    sys.stderr.write(msg)
+    sys.exit()
+    
+def main():
+
+    out_fname = sys.argv[1]
+    in_fname = sys.argv[2]
+    chr_col = int(sys.argv[3])-1
+    coord_col = int(sys.argv[4])-1
+    track_type = sys.argv[5]
+    if track_type == 'coverage' or track_type == 'both': 
+        coverage_col = int(sys.argv[6])-1
+        cname = sys.argv[7]
+        cdescription = sys.argv[8]
+        ccolor = sys.argv[9].replace('-',',')
+        cvisibility = sys.argv[10]
+    if track_type == 'snp' or track_type == 'both':
+        if track_type == 'both':
+            j = 5
+        else:
+            j = 0 
+        #sname = sys.argv[7+j]
+        sdescription = sys.argv[6+j]
+        svisibility = sys.argv[7+j]
+        #ref_col = int(sys.argv[10+j])-1
+        read_col = int(sys.argv[8+j])-1
+    
+
+    # Sort the input file based on chromosome (alphabetically) and start co-ordinates (numerically)
+    sorted_infile = tempfile.NamedTemporaryFile()
+    try:
+        os.system("sort -k %d,%d -k %dn -o %s %s" %(chr_col+1,chr_col+1,coord_col+1,sorted_infile.name,in_fname))
+    except Exception, exc:
+        stop_err( 'Initialization error -> %s' %str(exc) )
+
+    #generate chr list
+    sorted_infile.seek(0)
+    chr_vals = []
+    for line in file( sorted_infile.name ):
+        line = line.strip()
+        if not(line):
+            continue
+        try:
+            fields = line.split('\t')
+            chr = fields[chr_col]
+            if chr not in chr_vals:
+                chr_vals.append(chr)
+        except:
+            pass
+    if not(chr_vals):   
+        stop_err("Skipped all lines as invalid.")
+        
+    if track_type == 'coverage' or track_type == 'both':
+        if track_type == 'coverage':
+            fout = open( out_fname, "w" )
+        else:
+            fout = tempfile.NamedTemporaryFile()
+        fout.write('''track type=wiggle_0 name="%s" description="%s" color=%s visibility=%s\n''' \
+                      % ( cname, cdescription, ccolor, cvisibility ))
+    if track_type == 'snp' or track_type == 'both':
+        fout_a = tempfile.NamedTemporaryFile()
+        fout_t = tempfile.NamedTemporaryFile()
+        fout_g = tempfile.NamedTemporaryFile()
+        fout_c = tempfile.NamedTemporaryFile()
+        fout_ref = tempfile.NamedTemporaryFile()
+        
+        fout_a.write('''track type=wiggle_0 name="%s" description="%s" color=%s visibility=%s\n''' \
+                      % ( "Track A", sdescription, '255,0,0', svisibility ))
+        fout_t.write('''track type=wiggle_0 name="%s" description="%s" color=%s visibility=%s\n''' \
+                      % ( "Track T", sdescription, '0,255,0', svisibility ))
+        fout_g.write('''track type=wiggle_0 name="%s" description="%s" color=%s visibility=%s\n''' \
+                      % ( "Track G", sdescription, '0,0,255', svisibility ))
+        fout_c.write('''track type=wiggle_0 name="%s" description="%s" color=%s visibility=%s\n''' \
+                      % ( "Track C", sdescription, '255,0,255', svisibility ))
+        
+        
+    sorted_infile.seek(0)
+    for line in file( sorted_infile.name ):
+        line = line.strip()
+        if not(line):
+            continue
+        try:
+            fields = line.split('\t')
+            chr = fields[chr_col]
+            start = int(fields[coord_col])
+            assert start > 0
+        except:
+            continue
+        try:
+            ind = chr_vals.index(chr)    #encountered chr for the 1st time
+            del chr_vals[ind]
+            prev_start = ''
+            header = "variableStep chrom=%s\n" %(chr)
+            if track_type == 'coverage' or track_type == 'both':
+                coverage = int(fields[coverage_col])
+                line1 = "%s\t%s\n" %(start,coverage)
+                fout.write("%s%s" %(header,line1))
+            if track_type == 'snp' or track_type == 'both':
+                a = t = g = c = 0
+                fout_a.write("%s" %(header))
+                fout_t.write("%s" %(header))
+                fout_g.write("%s" %(header))
+                fout_c.write("%s" %(header))
+                try:
+                    #ref_nt = fields[ref_col].capitalize()
+                    read_nt = fields[read_col].capitalize()
+                    try:
+                        nt_ind = ['A','T','G','C'].index(read_nt)
+                        if nt_ind == 0:
+                            a+=1
+                        elif nt_ind == 1:
+                            t+=1
+                        elif nt_ind == 2:
+                            g+=1
+                        else:
+                            c+=1
+                    except ValueError:
+                        pass
+                except:
+                    pass
+            prev_start = start
+        except ValueError:
+            if start != prev_start:
+                if track_type == 'coverage' or track_type == 'both':
+                    coverage = int(fields[coverage_col])
+                    fout.write("%s\t%s\n" %(start,coverage)) 
+                if track_type == 'snp' or track_type == 'both':
+                    if a:
+                        fout_a.write("%s\t%s\n" %(prev_start,a))
+                    if t:
+                        fout_t.write("%s\t%s\n" %(prev_start,t))
+                    if g:
+                        fout_g.write("%s\t%s\n" %(prev_start,g))
+                    if c:
+                        fout_c.write("%s\t%s\n" %(prev_start,c))
+                    a = t = g = c = 0
+                    try:
+                        #ref_nt = fields[ref_col].capitalize()
+                        read_nt = fields[read_col].capitalize()
+                        try:
+                            nt_ind = ['A','T','G','C'].index(read_nt)
+                            if nt_ind == 0:
+                                a+=1
+                            elif nt_ind == 1:
+                                t+=1
+                            elif nt_ind == 2:
+                                g+=1
+                            else:
+                                c+=1
+                        except ValueError:
+                            pass
+                    except:
+                        pass
+                prev_start = start
+            else:
+                if track_type == 'snp' or track_type == 'both':
+                    try:
+                        #ref_nt = fields[ref_col].capitalize()
+                        read_nt = fields[read_col].capitalize()
+                        try:
+                            nt_ind = ['A','T','G','C'].index(read_nt)
+                            if nt_ind == 0:
+                                a+=1
+                            elif nt_ind == 1:
+                                t+=1
+                            elif nt_ind == 2:
+                                g+=1
+                            else:
+                                c+=1
+                        except ValueError:
+                            pass
+                    except:
+                        pass
+    
+    if track_type == 'snp' or track_type == 'both':
+        if a:
+            fout_a.write("%s\t%s\n" %(prev_start,a))
+        if t:
+            fout_t.write("%s\t%s\n" %(prev_start,t))
+        if g:
+            fout_g.write("%s\t%s\n" %(prev_start,g))
+        if c:
+            fout_c.write("%s\t%s\n" %(prev_start,c))
+            
+        fout_a.seek(0)
+        fout_g.seek(0)
+        fout_t.seek(0)
+        fout_c.seek(0)    
+    
+    if track_type == 'snp':
+        os.system("cat %s %s %s %s >> %s" %(fout_a.name,fout_t.name,fout_g.name,fout_c.name,out_fname))
+    elif track_type == 'both':
+        fout.seek(0)
+        os.system("cat %s %s %s %s %s | cat > %s" %(fout.name,fout_a.name,fout_t.name,fout_g.name,fout_c.name,out_fname))
+if __name__ == "__main__":
+    main()
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